Alternatives and similar repositories for MutSig2CV

Users that are interested in MutSig2CV are comparing it to the libraries listed below

• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆61Updated 4 years ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 4 years ago
• broadinstitute / RNA_MUTECT_1.0-1
  ☆38Updated 5 years ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆41Updated last year
• broadinstitute / gistic2
  Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
  ☆51Updated 3 years ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated 2 months ago
• McGranahanLab / TcellExTRECT
  ☆47Updated 4 months ago
• raphael-group / decifer
  DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell frac…
  ☆20Updated last year
• jason-weirather / hla-polysolver
  Fork of the Polysolver project
  ☆31Updated 5 years ago
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆29Updated 6 years ago
• ait5 / CNApp
  CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…
  ☆20Updated 5 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated 3 months ago
• ShixiangWang / Variants2Neoantigen
  A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
  ☆29Updated 5 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆31Updated last year
• Bioconductor / copy-number-analysis
  Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
  ☆21Updated 2 years ago
• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆34Updated 10 months ago
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆28Updated 2 years ago
• AlexandrovLab / SigProfilerTopography
  SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA re…
  ☆19Updated 3 months ago
• ding-lab / PanCanAtlasGermline
  ☆44Updated 6 years ago
• caravagnalab / mobster
  Model-based subclonal deconvolution from bulk sequencing.
  ☆33Updated 5 months ago
• PCAWG-11 / Evolution
  Code accompanying The Evolutionary history of 2,658 cancers
  ☆46Updated 4 years ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• ENCODE-DCC / mirna-seq-pipeline
  ☆17Updated 3 years ago
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆33Updated 2 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• XiDsLab / scFusion
  ☆21Updated 3 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• cancer-genomics / reproduce_lucas_wflow
  ☆28Updated last year
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆58Updated last week